Don't most schools still have to look at your MCAT score before they even consider your application?
So, what is the harm in applying "late" then? It's not like we have any advantage submitting it early, since obviously people who have taken their April MCAT will already be receiving secondaries and interview offers. On the other hand, if anything, people taking the August MCAT might get a few automatic secondaries. Big deal. Everyone gets one of those. If a person took the April MCAT and delayed their application till September, I can see this being a problem.
Would it really be a potential disadvantage to submit it in September or so? That way, there is still about 6 weeks for AMCAS to do its verification/processing. Also, as far as I know, you can send in transcripts even before your application is submitted. So, I still don't see how it would affect you other than maybe not knowing what school you're going to get into till early next year. Though, I think that would still be the case if you're taking the exam in August.